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pysb / pysb

Python framework for Systems Biology modeling
BSD 2-Clause "Simplified" License
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Stochastic simulation option? #423

Closed jadeshi closed 5 years ago

jadeshi commented 5 years ago

Would it be possible to add a functionality to perform stochastic simulations instead of only deterministic ones through the ODE solver (e.g. Gillespie's algorithm)?

alubbock commented 5 years ago

Hi, this functionality is already in PySB. We actually have interfaces to two implementations of Gillespie's Stochastic Simulation Algorithm (SSA): one based on StochKit and one based on BioNetGen.

Example using BioNetGen SSA: https://github.com/pysb/pysb/blob/v1.8.1/pysb/examples/run_bng_ssa_example.py Example using StochKit SSA: https://github.com/pysb/pysb/blob/v1.8.1/pysb/examples/run_tyson_oscillator_stochkit.py

Documentation on those interfaces is in the PySB documentation.

Hope that helps!

jadeshi commented 5 years ago

Perfect, this is exactly what I needed, thanks! I think it might be good to highlight these two examples, maybe in a small subsection of "Simulation and Analysis", since it may be useful for others as well!

alubbock commented 5 years ago

Updating the tutorial is a good idea. I've added that as a separate issue, #442

If you have further questions, please check out our chat room on gitter: https://gitter.im/pysb/pysb